Academic Journal
Analysis and uncertainty quantification of DNA fluorescence melt data: Applications of affine transformations.
| Τίτλος: | Analysis and uncertainty quantification of DNA fluorescence melt data: Applications of affine transformations. |
|---|---|
| Συγγραφείς: | Patrone PN; National Institute of Standards and Technology, USA. Electronic address: paul.patrone@nist.gov., Kearsley AJ; National Institute of Standards and Technology, USA., Majikes JM; National Institute of Standards and Technology, USA., Liddle JA; National Institute of Standards and Technology, USA. |
| Πηγή: | Analytical biochemistry [Anal Biochem] 2020 Oct 15; Vol. 607, pp. 113773. Date of Electronic Publication: 2020 Jun 08. |
| Τύπος έκδοσης: | Journal Article; Research Support, Non-U.S. Gov't |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Elsevier Country of Publication: United States NLM ID: 0370535 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1096-0309 (Electronic) Linking ISSN: 00032697 NLM ISO Abbreviation: Anal Biochem Subsets: MEDLINE |
| Imprint Name(s): | Publication: <2000- > : San Diego, CA : Elsevier Original Publication: Orlando Fl : Academic Press |
| Ιατρικοί όροι (MeSH): | DNA/*analysis, Databases, Factual ; Fluorescence Resonance Energy Transfer ; Models, Molecular ; Nucleic Acid Conformation ; Reproducibility of Results ; Spectrometry, Fluorescence ; Thermodynamics ; Transition Temperature |
| Περίληψη: | Fluorescence-based measurements are a standard tool for characterizing the thermodynamic properties of DNA systems. Nonetheless, experimental melt data obtained from polymerase chain-reaction (PCR) machines (for example) often leads to signals that vary significantly between datasets. In many cases, this lack of reproducibility has led to difficulties in analyzing results and computing reasonable uncertainty estimates. To address this problem, we propose a data analysis procedure based on constrained, convex optimization of affine transformations, which can determine when and how melt curves collapse onto one another. A key aspect of this approach is its ability to provide a reproducible and more objective measure of whether a collection of datasets yields a consistent "universal" signal according to an appropriate model of the raw signals. Importantly, integrating this validation step into the analysis hardens the measurement protocol by allowing one to identify experimental conditions and/or modeling assumptions that may corrupt a measurement. Moreover, this robustness facilitates extraction of thermodynamic information at no additional cost in experimental time. We illustrate and test our approach on experiments of Förster resonance energy transfer (FRET) pairs used study the thermodynamics of DNA loops. (Published by Elsevier Inc.) |
| References: | Clin Chem. 2003 Jun;49(6 Pt 1):853-60. (PMID: 12765979) Biochemistry. 1990 Sep 25;29(38):9029-39. (PMID: 1702995) Biophys J. 2009 Feb;96(3):1056-67. (PMID: 18849409) J Vis Exp. 2012 May 22;(63):e3998. (PMID: 22664923) Phys Life Rev. 2018 Aug;25:1-21. (PMID: 29170011) J Res Natl Inst Stand Technol. 2006 Apr 01;111(2):121-5. (PMID: 27274923) J Struct Biol. 1995 Sep-Oct;115(2):175-85. (PMID: 7577238) Nat Methods. 2014 Sep;11(9):895-8. (PMID: 25166868) Trends Genet. 2015 Feb;31(2):61-6. (PMID: 25579994) Bioconjug Chem. 2016 Mar 16;27(3):840-8. (PMID: 26895222) Nucleic Acids Res. 2020 Jun 4;48(10):5268-5280. (PMID: 32347943) Clin Chem. 2004 Oct;50(10):1748-54. (PMID: 15308590) Anal Biochem. 2017 Dec 15;539:90-95. (PMID: 29061329) Clin Chem. 2001 Apr;47(4):635-44. (PMID: 11274012) BMC Mol Biol. 2010 Sep 15;11:70. (PMID: 20840787) J Am Chem Soc. 2002 Jun 19;124(24):6950-6. (PMID: 12059218) PLoS One. 2012;7(3):e32866. (PMID: 22438886) |
| Grant Information: | 9999-NIST United States ImNIST Intramural NIST DOC |
| Substance Nomenclature: | 9007-49-2 (DNA) |
| Entry Date(s): | Date Created: 20200612 Date Completed: 20210222 Latest Revision: 20250530 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC7961812 |
| DOI: | 10.1016/j.ab.2020.113773 |
| PMID: | 32526200 |
| Βάση Δεδομένων: | MEDLINE |
| ISSN: | 1096-0309 |
|---|---|
| DOI: | 10.1016/j.ab.2020.113773 |